Job ID = 14520987 SRX = ERX4123665 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4592062 spots for ERR4157920/ERR4157920.sra Written 4592062 spots for ERR4157920/ERR4157920.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:53 4592062 reads; of these: 4592062 (100.00%) were unpaired; of these: 857300 (18.67%) aligned 0 times 3148168 (68.56%) aligned exactly 1 time 586594 (12.77%) aligned >1 times 81.33% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1288428 / 3734762 = 0.3450 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:17:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:12: 1000000 INFO @ Sat, 15 Jan 2022 20:17:18: 2000000 INFO @ Sat, 15 Jan 2022 20:17:20: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:17:20: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:17:20: #1 total tags in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:17:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:17:20: #1 tags after filtering in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:17:20: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:21: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:17:21: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:21: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:17:21: #2 alternative fragment length(s) may be 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 bps INFO @ Sat, 15 Jan 2022 20:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.05_model.r WARNING @ Sat, 15 Jan 2022 20:17:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:17:21: #2 You may need to consider one of the other alternative d(s): 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 WARNING @ Sat, 15 Jan 2022 20:17:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:17:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:21: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:17:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:41: 1000000 INFO @ Sat, 15 Jan 2022 20:17:49: 2000000 INFO @ Sat, 15 Jan 2022 20:17:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:17:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:17:52: #1 total tags in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:17:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:17:52: #1 tags after filtering in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:17:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:52: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:17:52: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:52: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:17:52: #2 alternative fragment length(s) may be 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 bps INFO @ Sat, 15 Jan 2022 20:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.10_model.r WARNING @ Sat, 15 Jan 2022 20:17:52: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:17:52: #2 You may need to consider one of the other alternative d(s): 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 WARNING @ Sat, 15 Jan 2022 20:17:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:17:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:18:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:18:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:18:11: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:18:18: 2000000 INFO @ Sat, 15 Jan 2022 20:18:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:18:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:18:21: #1 total tags in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:18:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:18:21: #1 tags after filtering in treatment: 2446334 INFO @ Sat, 15 Jan 2022 20:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:18:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:21: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:18:21: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:18:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:21: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:18:21: #2 alternative fragment length(s) may be 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 bps INFO @ Sat, 15 Jan 2022 20:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123665/ERX4123665.20_model.r WARNING @ Sat, 15 Jan 2022 20:18:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:18:21: #2 You may need to consider one of the other alternative d(s): 0,14,24,55,80,83,86,92,122,152,204,226,270,315,380,402,479,510,531,565,597 WARNING @ Sat, 15 Jan 2022 20:18:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:18:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it022/job_scripts/14520987: line 297: 29088 Terminated MACS $i /var/spool/uge/it022/job_scripts/14520987: line 297: 29235 Terminated MACS $i /var/spool/uge/it022/job_scripts/14520987: line 297: 30432 Terminated MACS $i ls: cannot access ERX4123665.05.bed: No such file or directory mv: cannot stat ‘ERX4123665.05.bed’: No such file or directory mv: cannot stat ‘ERX4123665.05.bb’: No such file or directory ls: cannot access ERX4123665.10.bed: No such file or directory mv: cannot stat ‘ERX4123665.10.bed’: No such file or directory mv: cannot stat ‘ERX4123665.10.bb’: No such file or directory ls: cannot access ERX4123665.20.bed: No such file or directory mv: cannot stat ‘ERX4123665.20.bed’: No such file or directory mv: cannot stat ‘ERX4123665.20.bb’: No such file or directory